tbuckley/cabot-search huggingface dataset:
The Blursday database as a resource to study subjective temporalities during COVID-19
Authors: Maximilien Chaumon, Pier-Alexandre Rioux, Sophie K. Herbst, Ignacio Spiousas, Sebastian L. Kübel, Elisa M. Gallego Hiroyasu, Şerife Leman Runyun, Luigi Micillo, Vassilis Thanopoulos, Esteban Mendoza-Duran, Anna Wagelmans, Ramya Mudumba, Ourania Tachmatzidou, Nicola Cellini, Arnaud D’Argembeau, Anne Giersch, Simon Grondin, Claude Gronfier, Federico Alvarez Igarzábal, André Klarsfeld, Ljubica Jovanovic, Rodrigo Laje, Elisa Lannelongue, Giovanna Mioni, Cyril Nicolaï, Narayanan Srinivasan, Shogo Sugiyama, Marc Wittmann, Yuko Yotsumoto, Argiro Vatakis, Fuat Balcı, Virginie van Wassenhove
Journal: Nature Human Behaviour (2022)

The COVID-19 pandemic and associated lockdowns triggered worldwide changes in the daily routines of human experience. The Blursday database provides repeated measures of subjective time and related processes from participants in nine countries tested on 14 questionnaires and 15 behavioural tasks during the COVID-19 pandemic. A total of 2,840 participants completed at least one task, and 439 participants completed all tasks in the first session. The database and all data collection tools are accessible to researchers for studying the effects of social isolation on temporal information processing, time perspective, decision-making, sleep, metacognition, attention, memory, self-perception and mindfulness. Blursday includes quantitative statistics such as sleep patterns, personality traits, psychological well-being and lockdown indices. The database provides quantitative insights on the effects of lockdown (stringency and mobility) and subjective confinement on time perception (duration, passage of time and temporal distances). Perceived isolation affects time perception, and we report an inter-individual central tendency effect in retrospective duration estimation. The Blursday database contains repeated measures of subjective time and related processes collected during the COVID-19 pandemic. The more isolated individuals felt, the slower time seemed to pass.
Non-invasive monitoring of blood oxygenation in human placentas via concurrent diffuse optical spectroscopy and ultrasound imaging
Authors: Lin Wang, Jeffrey M. Cochran, Tiffany Ko, Wesley B. Baker, Kenneth Abramson, Lian He, David R. Busch, Venki Kavuri, Rebecca L. Linn, Samuel Parry, Arjun G. Yodh, Nadav Schwartz
Journal: Nature Biomedical Engineering (2022)
JHEP at a glance (September 2022)
Authors: Guido Baselli, Oveis Jamialahmadi, Serena Pelusi, Giorgio Soardo, Daniele Prati, Stefano Romeoluca, V Valenti, Xiaoxiao Jiang, Sam Fulte, Fengyan Deng, Nicholas Davidson, Wen-Xing Ding, Hong- Min Ni
Journal: Journal of Hepatology (2022)
Matched related transplantation versus immunosuppressive therapy plus eltrombopag for first-line treatment of severe aplastic anemia: a multicenter, prospective study
Authors: Limin Liu, Meiqing Lei, Rong Fu, Bing Han, Xin Zhao, Rongrong Liu, Yanming Zhang, Wenjing Jiao, Miao Miao, Fengkui Zhang, Liansheng Zhang, Depei Wu
Journal: Journal of Hematology & Oncology (2022)

Abstract This study prospectively compared the efficacy and safety between matched related donor-hematopoietic stem cell transplantation (MRD-HSCT) ( n = 108) and immunosuppressive therapy (IST) plus eltrombopag (EPAG) (IST + EPAG) ( n = 104) to determine whether MRD-HSCT was still superior as a front-line treatment for patients with severe aplastic anemia (SAA). Compared with IST + EPAG group, patients in the MRD-HSCT achieved faster transfusion independence, absolute neutrophil count ≥ 1.0 × 10 9 /L ( P &lt; 0.05), as well as high percentage of normal blood routine at 6-month (86.5% vs. 23.7%, P &lt; 0.001). In the MRD-HSCT and IST + EPAG groups, 3-year overall survival (OS) was 84.2 ± 3.5% and 89.7 ± 3.1% ( P = 0.164), whereas 3-year failure-free survival (FFS) was 81.4 ± 4.0% and 59.1 ± 4.9% ( P = 0.002), respectively. Subgroup analysis indicated that the FFS of the MRD-HSCT was superior to that of the IST + EPAG among patients aged &lt; 40 years old (81.0 ± 4.6% vs. 63.7 ± 6.5%, P = 0.033), and among patients with vSAA (86.1 ± 5.9% vs. 54.9 ± 7.9%, P = 0.003), while the 3-year OS of the IST + EPAG was higher than that of the MRD-HSCT among the patient aged ≥ 40 years old (100.0 ± 0.0% vs. 77.8 ± 9.8%, P = 0.036). Multivariate analysis showed that first-line MRD-HSCT treatment was associated favorably with normal blood results at 6-month and FFS ( P &lt; 0.05). These outcomes suggest that MRD-HSCT remains the preferred first-line option for SAA patients aged &lt; 40 years old or with vSAA even in the era of EPAG.
Epidemiology of Lyme borreliosis based on outpatient claims data of all people with statutory health insurance, Germany, 2019
Authors: Manas K Akmatov, Jakob Holstiege, Lotte Dammertz, Joachim Heuer, Claudia Kohring, Martin Lotto-Batista, Friedrich Boeing, Stéphane Ghozzi, Stefanie Castell, Jörg Bätzing
Journal: Eurosurveillance (2022)

Introduction Evidence of nationwide and regional morbidity of Lyme borreliosis (LB) in Germany is lacking. Aims We calculated the total number of incident LB cases in Germany in 2019, compared regional variations, investigated the extent of possible under-reporting in notification data and examined the association between high incidence areas and land cover composition. Methods We used outpatient claims data comprising information for people with statutory health insurance who visited a physician at least once between 2010 and 2019 in Germany (n = 71,411,504). The ICD-10 code A69.2 was used to identify incident LB patients. Spatial variations of LB were assessed by means of Global and Local Moran’s Index at district level. Notification data were obtained for nine federal states with mandatory notification from the Robert Koch Institute (RKI). Results Of all insured, 128,177 were diagnosed with LB in 2019, corresponding to an incidence of 179 per 100,000 insured. The incidence varied across districts by a factor of 16 (range: 40–646 per 100,000). We identified four spatial clusters with high incidences. These clusters were associated with a significantly larger proportion of forests and agricultural areas than low incidence clusters. In 2019, 12,264 LB cases were reported to the RKI from nine federal states, while 69,623 patients with LB were found in claims data for those states. This difference varied considerably across districts. Conclusions These findings serve as a solid basis for regionally tailored population-based intervention programmes and can support modelling studies assessing the development of LB epidemiology under various climate change scenarios.
Letter by Benali et al Regarding Article, “Does Timing of Ventricular Tachycardia Ablation Affect Prognosis in Patients With an Implantable Cardioverter Defibrillator? Results From the Multicenter Randomized PARTITA Trial”
Authors: Karim Benali, Charles Guenancia, Raphaël P. Martins
Journal: Circulation (2022)
Immunomodulation of MiRNA-223-based nanoplatform for targeted therapy in retinopathy of prematurity
Authors: Keke Huang, Zhiqing Lin, Yuanyuan Ge, Xuhao Chen, Yining Pan, Ziru Lv, Xiaoting Sun, Hao Yu, Jiangfan Chen, Qingqing Yao
Journal: Journal of Controlled Release (2022)
Magnetic beads for the evaluation of drug release from biotinylated polymeric micelles in biological media
Authors: Yan Wang, Marcel H. Fens, Nicky C.H. van Kronenburg, Yang Shi, Twan Lammers, Michal Heger, Cornelus F. van Nostrum, Wim E. Hennink
Journal: Journal of Controlled Release (2022)

To improve the reliability of in vitro release studies of drug delivery systems, we developed a novel in vitro method for the evaluation of drug release from polymeric micelles in complex biological media. Polymeric micelles based on poly(N-2-hydroxypropyl methacrylamide)-block-poly(N-2-benzoyloxypropyl methacrylamide) (p(HPMAm)-b-p(HPMAm-Bz)) of which 10% of the chains was functionalized with biotin at the p(HPMAm) terminus were prepared using a solvent extraction method. The size of the micelles when loaded with a hydrophobic agent, namely paclitaxel (a clinically used cytostatic drug) or curcumin (a compound with multiple pharmacological activities), was around 65 nm. The biotin decoration allowed the binding of the micelles to streptavidin-coated magnetic beads which occurred within 10 min and reached a binding efficiency of 90 ± 6%. Drug release in different media was studied after the magnetic separation of micelles bound to the streptavidin-coated beads, by determination of the released drug in the media as well as the retained drug in the micellar fraction bound to the beads. The in vitro release of paclitaxel and curcumin at 37 °C in PBS, PBS containing 2% v/v Tween 80, PBS containing 4.5% w/v bovine serum albumin, mouse plasma, and whole mouse blood was highly medium-dependent. In all media studied, paclitaxel showed superior micellar retention compared to curcumin. Importantly, the presence of serum proteins accelerated the release of both paclitaxel and curcumin. The results presented in this study show great potential for predicting drug release from nanomedicines in biological media which in turn is crucial for their further pharmaceutical development.
CHDbase: A Comprehensive Knowledgebase for Congenital Heart Disease-Related Genes and Clinical Manifestations
Authors: Wei-Zhen Zhou, Wenke Li, Huayan Shen, Ruby W. Wang, Wen Chen, Yujing Zhang, Qingyi Zeng, Hao Wang, Meng Yuan, Ziyi Zeng, Jinhui Cui, Chuan-Yun Li, Fred Y. Ye, Zhou Zhou
Journal: Genomics Proteomics & Bioinformatics (2022)

Abstract Congenital heart disease (CHD) is one of the most common causes of major birth defects, with a prevalence of 1%. Although an increasing number of studies have reported the etiology of CHD, the findings scattered throughout the literature are difficult to retrieve and utilize in research and clinical practice. We therefore developed CHDbase, an evidence-based knowledgebase of CHD-related genes and clinical manifestations manually curated from 1114 publications, linking 1124 susceptibility genes and 3591 variations to more than 300 CHD types and related syndromes. Metadata such as the information of each publication and the selected population and samples, the strategy of studies, and the major findings of studies were integrated with each item of the research record. We also integrated functional annotations through parsing ∼ 50 databases/tools to facilitate the interpretation of these genes and variations in disease pathogenicity. We further prioritized the significance of these CHD-related genes with a gene interaction network approach and extracted a core CHD sub-network with 163 genes. The clear genetic landscape of CHD enables the phenotype classification based on the shared genetic origin. Overall, CHDbase provides a comprehensive and freely available resource to study CHD susceptibilities, supporting a wide range of users in the scientific and medical communities. CHDbase is accessible at http://chddb.fwgenetics.org.
Obstetric fistula in Bangladesh: estimates from a national survey with clinical validation correction
Authors: Saifuddin Ahmed, Sian Louise Curtis, Kanta Jamil, Quamrun Nahar, Mizanur Rahman, SK Nazmul Huda, Imteaz Ibne Mannan, Shusmita Khan, Anadil Alam, Emily H Weaver, Shams El Arifeen
Journal: The Lancet Global Health (2022)

Obstetric fistula, which develops after a prolonged or obstructed labour, is preventable and treatable. However, many women are still afflicted with the condition and remain untreated in low-income and middle-income countries. Concerns have also been raised that an increasing trend of caesarean sections is increasing the risk and share of iatrogenic obstetric fistula in these countries. The true prevalence of this condition is not known, which makes it difficult for health planners and policy makers to develop appropriate national health strategies to address the problem. The estimation of obstetric fistula with surveys is difficult because self-reporting of incontinence symptoms is subject to misclassification bias. In this study, we aimed to estimate the prevalence and burden of obstetric fistula in Bangladesh.
Baseline 18F-FDG PET/CT May Portend the Prognosis of Patients With Waldenström Macroglobulinemia/Lymphoplasmacytic Lymphoma After First-Line Treatment
Authors: Qingqing Pan, Xinxin Cao, Yaping Luo, Jian Li, Fang Li
Journal: Clinical Nuclear Medicine (2022)

The outcome of patients with Waldenström macroglobulinemia/lymphoplasmacytic lymphoma (WM/LPL) is variable. We aim to study if baseline 18 F-FDG PET/CT has some prognostic significance in WM/LPL.Thirty-three patients with newly diagnosed WM/LPL who underwent baseline 18 F-FDG PET/CT and received active treatment thereafter were recruited in this retrospective study. Semiquantitative indices of baseline 18 F-FDG PET/CT were measured as total lesion glycolysis (TLG), metabolic tumor volume (MTV), and SUV max . The patients were followed up for at least 3 years or until reaching the endpoint, which were defined as progression-free survival (PFS) and the time to next treatment (TTNT).The overall response rate of the first-line treatment in the recruited patients was 84.8% (28/33). The 3-year PFS and overall survival rates were 56.3% and 89.3%, respectively. Patients with PFS <36 months and TTNT <36 months showed TLG and MTV significantly higher than those with PFS ≥36 months and TTNT ≥36 months ( P < 0.05). SUV max in patients with PFS <36 months was significantly higher than those with PFS ≥36 months ( P = 0.033). Receiver operating characteristic analysis demonstrated that cutoff values of TLG >291.28 SUVbw * mL, MTV >108.78 mL, and SUV max >3.16 were optimal for predicting PFS <36 months. Kaplan-Meier analysis showed that TLG >291.28 SUVbw * mL and MTV >108.78 mL were predictive for shorter PFS ( P = 0.003) and TTNT ( P = 0.002). In multivariate analysis, TLG >291.28 SUVbw * mL and MTV >108.78 mL were independent predictors for shorter PFS (hazard ratio, 3.06; 95% confidence interval, 1.09-8.57; P = 0.033) and TTNT (hazard ratio, 10.01; 95% confidence interval, 2.56-39.22; P = 0.001).The metabolic indices of TLG and MTV in baseline 18 F-FDG PET/CT were independent prognostic factors to predict PFS and TTNT in patients with WM/LPL.
Defining elimination as a public health problem for schistosomiasis control programmes: beyond prevalence of heavy-intensity infections
Authors: Ryan E Wiegand, Fiona M Fleming, Sake J de Vlas, Maurice R Odiere, Safari Kinung'hi, Charles H King, Darin Evans, Michael D French, Susan P Montgomery, Anne Straily, Jürg Utzinger, Penelope Vounatsou, W Evan Secor
Journal: The Lancet Global Health (2022)

WHO's 2021-30 road map for neglected tropical diseases (NTDs) outlines disease-specific and cross-cutting targets for the control, elimination, and eradication of NTDs in affected countries. For schistosomiasis, the criterion for elimination as a public health problem (EPHP) is defined as less than 1% prevalence of heavy-intensity infections (ie, ≥50 Schistosoma haematobium eggs per 10 mL of urine or ≥400 Schistosoma mansoni eggs per g of stool). However, we believe the evidence supporting this definition of EPHP is inadequate and the shifting distribution of schistosomiasis morbidity towards more subtle, rather than severe, morbidity in the face of large-scale control programmes requires guidelines to be adapted. In this Viewpoint, we outline the need for more accurate measures to develop a robust evidence-based monitoring and evaluation framework for schistosomiasis. Such a framework is crucial for achieving the goal of widespread EPHP of schistosomiasis and to meet the WHO road map targets. We encourage use of overall prevalence of schistosome infection (instead of the prevalence of heavy-intensity infections), development of species-dependent and age-dependent morbidity markers, and construction of a standardised monitoring and evaluation protocol.
“Hood Sign” in Nuclear Medicine: An Unusual Presentation of Mantle Cell Lymphoma as Detected on FDG PET/CT
Authors: Anjali Prakash, Nilendu Purandare, Sneha Shah, Archi Agrawal, Ameya Puranik, Venkatesh Rangarajan
Journal: Clinical Nuclear Medicine (2022)

Abstract Mantle cell lymphoma is a rare and aggressive non-Hodgkin lymphoma with a high propensity for extranodal involvement, typically seen in the liver, marrow, and gastrointestinal system. Being an FDG-avid disease and a sensitive modality for detecting both nodal and extranodal disease, FDG PET/CT is recommended in the workup of mantle cell lymphoma. We present a rare pattern of cutaneous involvement of the head-neck region in a patient with mantle cell lymphoma, which can be described on FDG PET/CT as a “hood sign.”
Safety and immunogenicity of a typhoid conjugate vaccine among children aged 9 months to 12 years in Malawi: a nested substudy of a double-blind, randomised controlled trial
Authors: Nginache Nampota-Nkomba, Osward M Nyirenda, Lameck Khonde, Victoria Mapemba, Maurice Mbewe, John M Ndaferankhande, Harrison Msuku, Clemens Masesa, Theresa Misiri, Felistas Mwakiseghile, Priyanka D Patel, Pratiksha Patel, Ifayet Johnson-Mayo, Marcela F Pasetti, Robert S Heyderman, J Kathleen Tracy, Shrimati Datta, Yuanyuan Liang, Kathleen M Neuzil, Melita A Gordon, Matthew B Laurens
Journal: The Lancet Global Health (2022)

Typhoid fever is a substantial public health problem in Africa, yet there are few clinical trials of typhoid conjugate vaccine (TCV). We assessed immunogenicity and safety of Typbar TCV in Malawi.
COVID‐19 metabolism: Mechanisms and therapeutic targets
Authors: Tianshi Wang, Ying Cao, Haiyan Zhang, Zihao Wang, Cheuk Him Man, Yunfan Yang, Lingchao Chen, Shuangnian Xu, Xiaojing Yan, Quan Zheng, Yi‐Ping Wang
Journal: MedComm (2022)

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) dysregulates antiviral signaling, immune response, and cell metabolism in human body. Viral genome and proteins hijack host metabolic network to support viral biogenesis and propagation. However, the regulatory mechanism of SARS‐CoV‐2‐induced metabolic dysfunction has not been elucidated until recently. Multiomic studies of coronavirus disease 2019 (COVID‐19) revealed an intensive interaction between host metabolic regulators and viral proteins. SARS‐CoV‐2 deregulated cellular metabolism in blood, intestine, liver, pancreas, fat, and immune cells. Host metabolism supported almost every stage of viral lifecycle. Strikingly, viral proteins were found to interact with metabolic enzymes in different cellular compartments. Biochemical and genetic assays also identified key regulatory nodes and metabolic dependencies of viral replication. Of note, cholesterol metabolism, lipid metabolism, and glucose metabolism are broadly involved in viral lifecycle. Here, we summarized the current understanding of the hallmarks of COVID‐19 metabolism. SARS‐CoV‐2 infection remodels host cell metabolism, which in turn modulates viral biogenesis and replication. Remodeling of host metabolism creates metabolic vulnerability of SARS‐CoV‐2 replication, which could be explored to uncover new therapeutic targets. The efficacy of metabolic inhibitors against COVID‐19 is under investigation in several clinical trials. Ultimately, the knowledge of SARS‐CoV‐2‐induced metabolic reprogramming would accelerate drug repurposing or screening to combat the COVID‐19 pandemic.
18F-FDG PET/CT in Urethral Metastases From Bladder Cancer
Authors: Ediz Beyhan, Sevim Baykal Koca, Uğur Yücetaş, Tevfik Fikret Çermik, Nurhan Ergül
Journal: Clinical Nuclear Medicine (2022)

Urethral metastasis of bladder cancer after surgery is rare. We present a 63-year-old man who had surgery for invasive bladder carcinoma and prostate adenocarcinoma 4 years ago and referred for urethral hemorrhage. 18 F-FDG PET/CT was performed for restaging and showed intense linear 18 F-FDG activity in the proximal urethra. The patient underwent urethrectomy, and histopathology determined urethral metastasis.
Income differences in COVID-19 incidence and severity in Finland among people with foreign and native background: A population-based cohort study of individuals nested within households
Authors: Sanni Saarinen, Heta Moustgaard, Hanna Remes, Riikka Sallinen, Pekka Martikainen
Journal: PLoS Medicine (2022)

Although intrahousehold transmission is a key source of Coronavirus Disease 2019 (COVID-19) infections, studies to date have not analysed socioeconomic risk factors on the household level or household clustering of severe COVID-19. We quantify household income differences and household clustering of COVID-19 incidence and severity.We used register-based cohort data with individual-level linkage across various administrative registers for the total Finnish population living in working-age private households (N = 4,315,342). Incident COVID-19 cases (N = 38,467) were identified from the National Infectious Diseases Register from 1 July 2020 to 22 February 2021. Severe cases (N = 625) were defined as having at least 3 consecutive days of inpatient care with a COVID-19 diagnosis and identified from the Care Register for Health Care between 1 July 2020 and 31 December 2020. We used 2-level logistic regression with individuals nested within households to estimate COVID-19 incidence and case severity among those infected. Adjusted for age, sex, and regional characteristics, the incidence of COVID-19 was higher (odds ratio [OR] 1.67, 95% CI 1.58 to 1.77, p < 0.001, 28.4% of infections) among individuals in the lowest household income quintile than among those in the highest quintile (18.9%). The difference attenuated (OR 1.23, 1.16 to 1.30, p < 0.001) when controlling for foreign background but not when controlling for other household-level risk factors. In fact, we found a clear income gradient in incidence only among people with foreign background but none among those with native background. The odds of severe illness among those infected were also higher in the lowest income quintile (OR 1.97, 1.52 to 2.56, p < 0.001, 28.0% versus 21.6% in the highest quintile), but this difference was fully attenuated (OR 1.08, 0.77 to 1.52, p = 0.64) when controlling for other individual-level risk factors-comorbidities, occupational status, and foreign background. Both incidence and severity were strongly clustered within households: Around 77% of the variation in incidence and 20% in severity were attributable to differences between households. The main limitation of our study was that the test uptake for COVID-19 may have differed between population subgroups.Low household income appears to be a strong risk factor for both COVID-19 incidence and case severity, but the income differences are largely driven by having foreign background. The strong household clustering of incidence and severity highlights the importance of household context in the prevention and mitigation of COVID-19 outcomes.